R help - Dec 2009 - read.affy.mixed - subscript out of bounds error

Hello,
I have a problem with read.affy.mixed function. I want to read in  
together a set of CEL files from chip types Affymettrix HGU133A_2 and  
HGU133_Plus_2. I have my files to be read in in one directory together  
with a white space delimited file describing them (covdesc). In this  
directory I give a command:

 > merge <- read.affy.mixed()
Error in merged[[i]] : subscript out of bounds
Error in cdfName(merged[[i]]) :
   error in evaluating the argument 'object' in selecting a method for  
function 'cdfName'
 > sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] hgu133a2.db_2.3.5      hgu133plus2probe_2.5.0  
hgu133plus2.db_2.3.5   org.Hs.eg.db_2.3.6
  [5] RSQLite_0.7-3          DBI_0.2-4               
hgu133a2probe_2.5.0    AnnotationDbi_1.8.1
  [9] hgu133a2cdf_2.5.0      hgu133plus2cdf_2.5.0    
simpleaffy_2.22.0      gcrma_2.18.0
[13] genefilter_1.28.2      affy_1.24.2            Biobase_2.6.0

loaded via a namespace (and not attached):
[1] affyio_1.14.0        annotate_1.24.0      Biostrings_2.14.8     
IRanges_1.4.9
[5] preprocessCore_1.8.0 splines_2.10.0       survival_2.35-7       
tools_2.10.0
[9] xtable_1.5-6

Thanks for your help!
Zuza

Hi Zuzanna --

Zuzanna wrote:
> Hello,
> I have a problem with read.affy.mixed function. I want to read in
> together a set of CEL files from chip types Affymettrix HGU133A_2 and
> HGU133_Plus_2. I have my files to be read in in one directory together
> with a white space delimited file describing them (covdesc). In this
> directory I give a command:
Please ask questions about Bioconductor packages on the Bioconductor
mailing list

  http://bioconductor.org/docs/mailList.html

my guess would be that 'covdesc' is not formatted properly, and that no
files are actually merged. You might try

  debug(read.affy.merged)
  read.affy.merged()

and step through as described in ?browser.

Martin
> 
>> merge <- read.affy.mixed()
> Error in merged[[i]] : subscript out of bounds
> Error in cdfName(merged[[i]]) :
>   error in evaluating the argument 'object' in selecting a method
for
> function 'cdfName'
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-apple-darwin9.8.0
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] hgu133a2.db_2.3.5      hgu133plus2probe_2.5.0
> hgu133plus2.db_2.3.5   org.Hs.eg.db_2.3.6
>  [5] RSQLite_0.7-3          DBI_0.2-4             
> hgu133a2probe_2.5.0    AnnotationDbi_1.8.1
>  [9] hgu133a2cdf_2.5.0      hgu133plus2cdf_2.5.0  
> simpleaffy_2.22.0      gcrma_2.18.0
> [13] genefilter_1.28.2      affy_1.24.2            Biobase_2.6.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        annotate_1.24.0      Biostrings_2.14.8   
> IRanges_1.4.9
> [5] preprocessCore_1.8.0 splines_2.10.0       survival_2.35-7     
> tools_2.10.0
> [9] xtable_1.5-6
> 
> Thanks for your help!
> Zuza
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793